
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms  101 (  101),  selected  101 , name T0304TS599_1-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304TS599_1-D1.T0304_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R      17      -       -           -
LGA    P      18      -       -           -
LGA    W      19      -       -           -
LGA    W      20      -       -           -
LGA    G      21      -       -           -
LGA    L      22      -       -           -
LGA    P      23      -       -           -
LGA    C      24      -       -           -
LGA    T      25      -       -           -
LGA    V      26      -       -           -
LGA    T      27      -       -           -
LGA    P      28      -       -           -
LGA    C      29      R      17          4.629
LGA    F      30      -       -           -
LGA    G      31      -       -           -
LGA    A      32      -       -           -
LGA    R      33      P      18          2.397
LGA    L      34      W      19          1.037
LGA    V      35      -       -           -
LGA    Q      36      W      20           #
LGA    E      37      G      21           #
LGA    G      38      -       -           -
LGA    N      39      L      22          4.279
LGA    R      40      P      23          2.108
LGA    L      41      C      24          1.544
LGA    H      42      T      25          2.000
LGA    Y      43      -       -           -
LGA    L      44      V      26          3.332
LGA    A      45      T      27          3.118
LGA    D      46      -       -           -
LGA    R      47      -       -           -
LGA    A      48      -       -           -
LGA    G      49      P      28           #
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      E      37           -
LGA    -       -      G      38           -
LGA    -       -      N      39           -
LGA    -       -      R      40           -
LGA    -       -      L      41           -
LGA    -       -      H      42           -
LGA    -       -      Y      43           -
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    I      50      I      50           #
LGA    R      51      R      51          3.633
LGA    G      52      G      52          3.105
LGA    L      53      L      53          3.903
LGA    F      54      F      54          1.118
LGA    S      55      S      55          1.451
LGA    D      56      D      56          3.274
LGA    A      57      A      57          3.483
LGA    D      58      D      58          1.383
LGA    A      59      A      59          1.145
LGA    Y      60      Y      60          2.057
LGA    H      61      H      61          0.956
LGA    L      62      L      62          0.956
LGA    D      63      D      63          1.818
LGA    Q      64      Q      64          1.560
LGA    A      65      A      65          1.396
LGA    F      66      F      66          2.271
LGA    P      67      P      67          1.609
LGA    L      68      L      68          0.422
LGA    L      69      L      69          1.681
LGA    M      70      M      70          1.714
LGA    K      71      K      71          0.758
LGA    Q      72      Q      72          1.762
LGA    L      73      L      73          1.888
LGA    E      74      E      74          0.514
LGA    L      75      L      75          2.123
LGA    M      76      M      76          2.745
LGA    L      77      L      77          1.349
LGA    T      78      T      78          1.715
LGA    S      79      S      79          3.419
LGA    G      80      -       -           -
LGA    E      81      G      80          4.433
LGA    L      82      E      81          1.947
LGA    N      83      -       -           -
LGA    P      84      -       -           -
LGA    R      85      -       -           -
LGA    H      86      L      82          3.568
LGA    Q      87      N      83          1.325
LGA    H      88      P      84          4.414
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    T      89      Q      87          4.653
LGA    V      90      H      88          5.285
LGA    T      91      T      89          3.363
LGA    L      92      V      90           -
LGA    Y      93      T      91           -
LGA    A      94      L      92           -
LGA    K      95      Y      93           -
LGA    G      96      A      94           -
LGA    L      97      K      95           -
LGA    T      98      G      96           -
LGA    C      99      L      97           -
LGA    K     100      T      98           -
LGA    A     101      -       -           -
LGA    D     102      -       -           -
LGA    T     103      -       -           -
LGA    L     104      -       -           -
LGA    S     105      -       -           -
LGA    S     106      -       -           -
LGA    C     107      -       -           -
LGA    D     108      -       -           -
LGA    Y     109      -       -           -
LGA    V     110      C      99          2.531
LGA    Y     111      K     100          0.689
LGA    L     112      A     101           #
LGA    A     113      D     102           -
LGA    V     114      T     103           -
LGA    Y     115      L     104           -
LGA    P     116      S     105           -
LGA    T     117      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    -       -      L     112           -
LGA    -       -      A     113           -
LGA    -       -      V     114           -
LGA    -       -      Y     115           -
LGA    -       -      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)  101  101    5.0     48    2.64    62.50     33.624     1.752

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.619713 * X  +  -0.600387 * Y  +   0.505462 * Z  +  44.062336
  Y_new =   0.616563 * X  +  -0.770923 * Y  +  -0.159774 * Z  +  30.291836
  Z_new =   0.485599 * X  +   0.212635 * Y  +   0.847927 * Z  +  38.772884 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.245704   -2.895889  [ DEG:    14.0778   -165.9222 ]
  Theta =  -0.507048   -2.634544  [ DEG:   -29.0517   -150.9483 ]
  Phi   =   2.358742   -0.782851  [ DEG:   135.1460    -44.8540 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0304TS599_1-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304TS599_1-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:  101  101   5.0   48   2.64   62.50  33.624
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS599_1-D1
PFRMAT TS                                                                       
TARGET T0304                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM     17  CA  ARG    17      54.302  38.666  38.426  1.00  0.00              
ATOM     18  CA  PRO    18      53.653  35.383  40.322  1.00  0.00              
ATOM     19  CA  TRP    19      50.267  34.558  38.883  1.00  0.00              
ATOM     20  CA  TRP    20      50.715  30.976  37.838  1.00  0.00              
ATOM     21  CA  GLY    21      48.916  30.414  34.707  1.00  0.00              
ATOM     22  CA  LEU    22      48.240  26.638  34.505  1.00  0.00              
ATOM     23  CA  PRO    23      45.282  25.760  32.369  1.00  0.00              
ATOM     24  CA  CYS    24      42.353  24.417  34.284  1.00  0.00              
ATOM     25  CA  THR    25      40.950  21.198  33.124  1.00  0.00              
ATOM     26  CA  VAL    26      37.780  20.066  34.922  1.00  0.00              
ATOM     27  CA  THR    27      37.475  16.362  35.939  1.00  0.00              
ATOM     28  CA  PRO    28      34.264  15.337  37.743  1.00  0.00              
ATOM     29  CA  CYS    29      35.763  14.153  41.033  1.00  0.00              
ATOM     30  CA  PHE    30      37.826  17.366  41.298  1.00  0.00              
ATOM     31  CA  GLY    31      35.128  19.870  40.254  1.00  0.00              
ATOM     32  CA  ALA    32      32.708  18.686  42.950  1.00  0.00              
ATOM     33  CA  ARG    33      35.556  19.033  45.451  1.00  0.00              
ATOM     34  CA  LEU    34      36.176  22.644  44.365  1.00  0.00              
ATOM     35  CA  VAL    35      32.463  23.535  44.720  1.00  0.00              
ATOM     36  CA  GLN    36      32.395  21.927  48.100  1.00  0.00              
ATOM     37  CA  GLU    37      35.518  23.768  49.373  1.00  0.00              
ATOM     38  CA  GLY    38      34.313  27.171  48.280  1.00  0.00              
ATOM     39  CA  ASN    39      36.805  27.845  45.537  1.00  0.00              
ATOM     40  CA  ARG    40      34.950  29.461  42.725  1.00  0.00              
ATOM     41  CA  LEU    41      35.951  28.409  39.245  1.00  0.00              
ATOM     42  CA  HIS    42      34.384  30.871  36.938  1.00  0.00              
ATOM     43  CA  TYR    43      32.893  32.040  33.729  1.00  0.00              
ATOM     44  CA  LEU    44      35.233  30.452  31.111  1.00  0.00              
ATOM     45  CA  ALA    45      35.108  27.191  33.121  1.00  0.00              
ATOM     46  CA  ASP    46      31.287  27.097  32.927  1.00  0.00              
ATOM     47  CA  ARG    47      31.108  27.640  29.176  1.00  0.00              
ATOM     48  CA  ALA    48      33.516  24.776  28.566  1.00  0.00              
ATOM     49  CA  GLY    49      31.733  22.315  30.844  1.00  0.00              
ATOM     50  CA  ILE    50      34.150  21.614  33.685  1.00  0.00              
ATOM     51  CA  ARG    51      34.364  17.855  33.597  1.00  0.00              
ATOM     52  CA  GLY    52      34.732  17.719  29.821  1.00  0.00              
ATOM     53  CA  LEU    53      37.098  20.451  28.916  1.00  0.00              
ATOM     54  CA  PHE    54      40.472  18.874  29.158  1.00  0.00              
ATOM     55  CA  SER    55      41.518  16.027  26.967  1.00  0.00              
ATOM     56  CA  ASP    56      43.433  13.496  29.059  1.00  0.00              
ATOM     57  CA  ALA    57      46.688  14.250  27.216  1.00  0.00              
ATOM     58  CA  ASP    58      46.386  17.965  27.981  1.00  0.00              
ATOM     59  CA  ALA    59      45.737  17.071  31.671  1.00  0.00              
ATOM     60  CA  TYR    60      49.069  15.169  31.699  1.00  0.00              
ATOM     61  CA  HIS    61      50.797  18.248  30.176  1.00  0.00              
ATOM     62  CA  LEU    62      49.161  20.576  32.727  1.00  0.00              
ATOM     63  CA  ASP    63      50.197  18.236  35.575  1.00  0.00              
ATOM     64  CA  GLN    64      53.796  18.561  34.473  1.00  0.00              
ATOM     65  CA  ALA    65      53.658  22.388  34.338  1.00  0.00              
ATOM     66  CA  PHE    66      51.940  22.701  37.672  1.00  0.00              
ATOM     67  CA  PRO    67      54.534  20.964  39.766  1.00  0.00              
ATOM     68  CA  LEU    68      57.177  23.451  38.492  1.00  0.00              
ATOM     69  CA  LEU    69      54.977  26.445  39.000  1.00  0.00              
ATOM     70  CA  MET    70      54.050  25.585  42.563  1.00  0.00              
ATOM     71  CA  LYS    71      57.667  25.017  43.490  1.00  0.00              
ATOM     72  CA  GLN    72      58.699  28.378  42.004  1.00  0.00              
ATOM     73  CA  LEU    73      55.876  30.116  43.813  1.00  0.00              
ATOM     74  CA  GLU    74      56.931  28.481  47.128  1.00  0.00              
ATOM     75  CA  LEU    75      60.541  29.573  46.653  1.00  0.00              
ATOM     76  CA  MET    76      59.331  33.147  45.987  1.00  0.00              
ATOM     77  CA  LEU    77      57.103  33.123  49.065  1.00  0.00              
ATOM     78  CA  THR    78      59.837  31.916  51.414  1.00  0.00              
ATOM     79  CA  SER    79      62.235  34.600  50.088  1.00  0.00              
ATOM     80  CA  GLY    80      59.996  37.600  50.432  1.00  0.00              
ATOM     81  CA  GLU    81      60.069  38.579  46.796  1.00  0.00              
ATOM     82  CA  LEU    82      56.352  38.636  46.368  1.00  0.00              
ATOM     83  CA  ASN    83      54.124  41.038  47.927  1.00  0.00              
ATOM     84  CA  PRO    84      51.533  41.499  50.496  1.00  0.00              
ATOM     85  CA  ARG    85      48.565  41.039  48.247  1.00  0.00              
ATOM     86  CA  HIS    86      49.880  37.749  46.738  1.00  0.00              
ATOM     87  CA  GLN    87      50.707  35.873  49.895  1.00  0.00              
ATOM     88  CA  HIS    88      48.909  32.663  49.211  1.00  0.00              
ATOM     89  CA  THR    89      45.683  33.976  47.595  1.00  0.00              
ATOM     90  CA  VAL    90      45.025  33.576  43.925  1.00  0.00              
ATOM     91  CA  THR    91      42.518  35.835  42.230  1.00  0.00              
ATOM     92  CA  LEU    92      40.913  34.809  39.122  1.00  0.00              
ATOM     93  CA  TYR    93      39.273  37.450  37.015  1.00  0.00              
ATOM     94  CA  ALA    94      36.504  36.458  34.568  1.00  0.00              
ATOM     95  CA  LYS    95      33.561  36.548  36.997  1.00  0.00              
ATOM     96  CA  GLY    96      35.267  36.577  40.332  1.00  0.00              
ATOM     97  CA  LEU    97      36.952  33.383  41.355  1.00  0.00              
ATOM     98  CA  THR    98      39.012  33.211  44.491  1.00  0.00              
ATOM     99  CA  CYS    99      41.581  30.536  44.938  1.00  0.00              
ATOM    100  CA  LYS   100      43.201  29.995  48.309  1.00  0.00              
ATOM    101  CA  ALA   101      46.881  29.007  48.065  1.00  0.00              
ATOM    102  CA  ASP   102      46.787  25.520  49.421  1.00  0.00              
ATOM    103  CA  THR   103      43.504  24.118  48.071  1.00  0.00              
ATOM    104  CA  LEU   104      43.932  25.201  44.449  1.00  0.00              
ATOM    105  CA  SER   105      47.476  23.826  44.372  1.00  0.00              
ATOM    106  CA  SER   106      46.609  20.415  45.804  1.00  0.00              
ATOM    107  CA  CYS   107      43.776  19.954  43.372  1.00  0.00              
ATOM    108  CA  ASP   108      45.410  20.882  40.131  1.00  0.00              
ATOM    109  CA  TYR   109      44.182  24.455  39.689  1.00  0.00              
ATOM    110  CA  VAL   110      45.917  27.337  37.881  1.00  0.00              
ATOM    111  CA  TYR   111      45.757  30.820  39.523  1.00  0.00              
ATOM    112  CA  LEU   112      45.328  33.994  37.573  1.00  0.00              
ATOM    113  CA  ALA   113      45.756  37.234  39.370  1.00  0.00              
ATOM    114  CA  VAL   114      43.725  40.234  38.309  1.00  0.00              
ATOM    115  CA  TYR   115      44.706  43.724  39.538  1.00  0.00              
ATOM    116  CA  PRO   116      42.226  46.558  39.451  1.00  0.00              
ATOM    117  CA  THR   117      43.526  49.533  37.567  1.00  0.00              
TER                                                                             
END
